help

Von: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> im Auftrag von freesurfer-request@nmr.mgh.harvard.edu <freesurfer-request@nmr.mgh.harvard.edu>
Gesendet: Donnerstag, 27. April 2017 19:24:57
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Freesurfer Digest, Vol 158, Issue 53
 
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Today's Topics:

   1. Last weeks to register for HCP Course 2017 (Jennifer Elam)
   2. the voxel in apar+aseg.mgh does not showing value from my
      parcellation table (Das S.)


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Message: 1
Date: Thu, 27 Apr 2017 12:16:42 -0500
From: Jennifer Elam <elam4hcp@gmail.com>
Subject: [Freesurfer] Last weeks to register for HCP Course 2017
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <CAJbMWh5GQ8zLtDdWHcnd2b=FvWbFMKteReS2YxiFvk3MGfu7Ow@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

It's not too late to register for the 2017 HCP Course: "Exploring the Human
Connectome"
<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstore.humanconnectome.org%2Fcourses%2F2017%2Fexploring-the-human-connectome.php&data=01%7C01%7Cbeckerjt%40pitt.edu%7C2a4dd6a90d924e4df57108d46bc180fb%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=2L5D2SmW5%2BArBZpn8YA2IIfc%2BU1XYDV8aoAIITW9FNc%3D&reserved=0>,
to be held June 19-23 at the Djavad Mowafagian Centre for Brain Health at
University of British Columbia (UBC) in Vancouver, BC, Canada!

FreeSurfer is a major part of the HCP structural processing pipeline and
has been critical to the processing of the project's over 1100 released
high quality imaging datasets.

Spaces for the course are limited and registration is on a first come,
first served basis.

May 17, 2017 is the deadline to reserve discounted UBC accommodations within
walking distance to the course venue:
https://reserve.ubcconferences.com/vancouver/availability.asp?hotelCode=%2A&startDate=06%2F16%2F2017&endDate=06%2F24%2F2017&adults=1&children=&rooms=1&requesttype=invBlockCode&code=G170618A

The 5-day intensive HCP course is a great opportunity to learn directly
from HCP investigators and designed for those interested in:

   - using data collected and distributed from the HCP young adult study
   - acquiring and analyzing HCP-style imaging and behavioral data at your
   own institution
   - processing your own non-HCP data using HCP pipelines and methods
   - using Connectome Workbench tools and sharing data using
   the BALSA imaging database
   - learning HCP multimodal neuroimaging analysis methods, including those
   that combine MEG and MRI data
   - exploring the HCP MMP 1.0 multimodal parcellation brain map
   and learning about how it can be used in your analyses
   - positioning yourself to capitalize on HCP-style data being distributed
   by the Connectome Coordinating Facility (CCF) from HCP development (healthy
   subjects ages 5-21) and aging (healthy subjects ages 35-90+) and
   Connectomes Related to Human Disease projects


See
https://store.humanconnectome.org/courses/2017/exploring-the-human-connectome.php
for more info.

If you have any questions, please contact us at:
hcpcourse@humanconnectome.org

We look forward to seeing you in Vancouver!

Best,
2017 HCP Course Staff
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Message: 2
Date: Thu, 27 Apr 2017 17:24:42 +0000
From: "Das S." <Sarbani.Das@soton.ac.uk>
Subject: [Freesurfer] the voxel in apar+aseg.mgh does not showing
        value from my parcellation table
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <97B5870E051A9548B7BAB625B7DC824AF0D955@SRV00047.soton.ac.uk>
Content-Type: text/plain; charset="iso-8859-1"

Dear Freesurfer Developer,
I am using freesurfer to create a equal zone parcellation on cortical surface.
I have used recon-all steps to create the aparc+aseg.mgz file. But in my aparc+aseg.mgz file I can't see the equal parcellation I have done.

Here are steps that I have followed:

 1. Divided the vertex point from the sphere.reg into equal numbers and assigned them to label files.This way I have created n number of label files, n/2 for left and n/2 for right sphere. The label file names are as below lh.node-lh-1.label ........

2. Then I run the mris_label2annot command to create the ?h.free40aparc.annot files. Before that I have created two color lookup table for left and right hemisphere.


mris_label2annot --s 100307 --h rh --no-unknown --ctab 100307/label/eq_parcellation_label/right/MyColorLUTright.txt --a rightaparc --ldir 100307/label/eq_parcellation_label/right

 mris_label2annot --s 100307 --h lh --no-unknown --ctab 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt --a leftaparc --ldir 100307/label/eq_parcellation_label/left

Content of ColorLUT.txt
801   node-lh-1                        70      130 180 0
802   node-lh-2                       245     245 245 0
803   node-lh-3                        205     62  78   0.....

3.  Then I am using the mris_ca_train to create the .gcs file.

  mris_ca_train -t  100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.annot 100307 100307/label/lh.leftaparc.gcs


 mris_ca_train -t  100307/label/eq_parcellation_label/right/MyColorLUTright.txt rh 100307/surf/rh.sphere.reg 100307/label/rh.rightaparc.annot 100307 100307/label/rh.righttaparc.gcs

4. then I am following the recon-all steps and call the mris_ca_label command as below:
  mris_ca_label -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt 100307 rh 100307/surf/rh.sphere.reg 100307/label/rh.righttaparc.gcs  100307/label/rh.aparc.annot
  mris_ca_label -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt 100307 lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.gcs  100307/label/lh.aparc.annot

5. Then I followed the rest of recon-all steps to create the apar+aseg.mgz file as below:
  recon-all -pial -subjid 100307
  recon-all -cortribbon -subjid 100307
  recon-all -parcstats -subjid 100307
  recon-all -pctsurfcon  -subjid 100307
  recon-all -hyporelabel  -subjid 100307
  recon-all -aparc2aseg  -subjid 100307


I am attaching my aparc+aseg.mgh file. Please guide me where I did wrong that the file is not reflecting valueof  my equal parcellation lookup table. I tried many ways but coundn't figure out. Any help will be much appreciated.
Thanks
Sarbani Das
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